I think, after 10+ years, it's getting obvious that I won't be able to complete this story the way I originally wanted to. Frankly, I don't even remember all the details of how it was going to get from this point to the end I envisioned, and my notes were lost a few computers ago. But to attempt to at least partially satisfy all those who have read and enjoyed this story, I'll try to give a basic outline of the high points that were supposed to occur in the last part.
At the end of the last chapter I posted, John is diverted into the wormhole environment where he met Einstein in the series. Since the Ancient who originally met John and took the form of his father Jack didn't die in this story, he's the one who meets John there rather than the more cryptic Einstein. The conversation is a combination of Jack's warnings and rants from Infinite Possibilities and Einstein's object lessons in Unrealized Realities. John is even shown the possible universe where he wasn't a Peacekeeper tech, where he stayed with the prisoners on Moya and ended up destroying the Command Carrier, which horrifies him since he now has friends and colleagues among the crew.
John learns more about how to find wormholes using the instinctive knowledge the Ancients gave him, and about how to successfully shield from them using a displacement engine, but also the danger of letting the knowledge into the wider world due to sheer destructive power.
Upon his return, his successful transit of the wormhole in his own ship is the evidence Grayza needs to shut down Scorpius' project as nonviable for PK craft. Scorpius objects, Grayza orders him arrested, Scorpius fails to get support from anyone in his crew other than Braca, then escapes and flees to a Leviathan and uses command override to direct it into the wormhole. Grayza orders the wormhole shut down in an attempt to stop him, but he gets in just before it collapses. The PKs presume Scorpius died in the collapse or from wormhole sickness like the other pilots, but we'll later learn he survived but the Leviathan was badly injured and went by instinct to the Leviathan burial space, where Scorpius meets Sikozu and partners with her.
Braca gets demoted and thrown in the brig for his attempt to help Scorpius, while Crichton gains Grayza's "interest". There was going to be some of the heppel oil date-rape of Crichton during the next chapter or so, which put strain on his relationship with Aeryn (more due to John's shame than to Aeryn feeling any sort of betrayal). John manages not to reveal anything except his knowledge of how to find natural wormholes and shield ships. (Prowler's can't be shielded but Marauders and larger ships can be. Carriers are too large to navigate a wormhole.) John gets promoted to second in command. Grayza tries to use Crichton's wormhole tech, incomplete as it is, as a bargaining point with the Scarrans, and when that fails, provokes a war.
John saves the carrier by having them flee into a wormhole against Grayza's orders. She tries to have him arrested. High command disagrees. Since Crichton saved the ship and Grayza got them into a war and almost lost them the carrier, they arrest her, promote him to captain, and send them back to the front to defend PK space using wormhole tech.
John releases Braca from the brig, restores his Lieutenant rank, and promotes him to second in command; he asks for his help, since John has no experience with commanding a PK carrier. They become friends.
War continues, with wormhole use allowing PKs to strike targets deep in Scarran space, while Scarrans destroy many Sebacean and other race's worlds. On one strike into Scarran space, Aeryn's marauder is apparently shot down over an ice world during the PK retreat, leading John to believe she's dead. He becomes cold and ruthless in his grief.
Scorpius later approaches the carrier with Sikozu, offering aid and Sikozu's intelligence about the Scarran empire. Braca recommends allowing them aboard. Both initally appear cooperative, with Scorpius revealing the secret of the crystherium flower, the Scarran dependence on it, and its limited locations of cultivation. Scorpius is injured or killed by Sikozu in her attempt to steal the wormhole tech for the Scarrans. She is caught, manages to kill Braca in the melee and is shot by Crichton. (Scene from prologue) Not sure if Scorpius survives or not...
Aeryn is still alive, uses her tech experience from the time she, John and Gilina were on the run to repair her ship, and manages to limp back to PK space, dodging Scarran patrols. Touching reunion, much crying ensues.
The Scarrans decimate the Breakaway colonies, specifically the Royal Planet, kill Empress Novia and destroy the statues of Katralla and Tyno. One of the palace servants manages to steal the largest remaining piece of Katralla's statue, and escape to PK space. He delivers it to Crichton, and informs him of what he wasn't told before, that his DNA was used to create a viable child for Katralla before she was turned into a statue. The statue piece might be able to be returned to flesh and the embryo transferred to a living host.
Crichton uses Scorpius' knowledge of chrystherium viable worlds to find several of them and destroy them using a displacement engine similar to the one in Infinite Possibilites to direct a chunk of solar material at the planet. Scarrans surrender, but PKs want Crichton's tech for their own use. Crais arrives with his armada to take it.
Jack returns, angry at Crichton's use of wormhole weapon tech, even if it wasn't the galaxy-destroying version. John explains that PKs now want it. Jack, John, Aeryn, and many of John's tech friends conspire to destroy the information and tech used for the wormhole weapon by first evacuating the carrier and then destroying it. They escape on Moya, find a wormhole and go to Earth.